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Okay, so I recently started using my EZ Flash again and I noticed that I was unable to save my games. Pokemon games display an error at start up (Battery has run dry) and Golden Sun The Lost Age says "Unable to detect backup memory." Note that I have already replaced the battery (soldered with the + (top) side of the battery facing up and connected to the upper solder connection on the pcb). I'm not sure what is wrong with it. I've been searching around and it could be possible that the SRAM is faulty. I have no way to test it to be sure because the SRAM test links lead to an ad site so I can't download it. I'm kind of wondering that the message from Golden Sun is pointing to the SRAM possibly. Note that I have replaced the files on the micro SD with a fresh and clean batch of files (EXPloader). I'm not the most technical person out there so I'm just looking for opinions on what it could be. In the end, I guess I could spend the cash for a new 3in1 but what are the chances that the battery could be old on those if the 3in1's are backstocked or are no longer being produced?

Edit: Also note that I have the 3in1 version 4 with EZ5C11 printed on the back of the pcb.

I don't know about golden sun personally but I believe the pokemon games will always return this error unless they're patched with GBATA (and there is no patch for emerald)
For those games, this is not much of a problem, and it can't be solved with the ez 3in1 (I think maybe the EZ-Flash 3 had RTC?) due to RTC support not being in the 3-in-1.
It sounds like you might not be patching the games at all before putting them on your 3in1, as what golden sun's complaining about is probably the same thing that pokemon LG/FR complain about, looking for a flash save chip when there isn't one.
While it is definitely possible for a battery to go dead after that many years, I doubt this is actually the issue here.

Okay...so apparently I might have fixed it... I was still using the 3in1 expansion by Rudolph rather than the EXPloader. I removed all of the previous files and pasted fresh exploader files. I played Golden Sun and saved at the first chance I got. I turned the system off and then started another game (Japanese Rhythm Tengoku) and restarted the system after completing the first minigame. Upon restart of exploader, I noticed that there was a .SAV in previous SRAM area on the bottom screen. So, I just went ahead and loaded up Golden Sun again and the save was still there! I removed the cartridge completely from the console so to be sure it is not just a power cycling thing or something where the data was being stored temporarily. So far I have started up both Golden Sun and Rhythm Tenogoku and they are retaining their saves! I'm really not sure what the issue was but I must have fixed it and I hope it stays fixed...lol.

I'm having this exact problem myself. I have opened my ez flash 3in1 V 2 times, once to check the charge of the battery, and again to check if the connections are good. The battery has 3.3V charge and all connections are okay, so I don't understand why I cannot use ANY save functions at all on my ez flash. Rumble works, ROMs that don't need to be initialized at the beginning work (Sonic Advance 1, 2 and 3 work, but not Pinball Party, for example), and I only got this to be able to play Sonic Advance 3 on my DS Lite cuz I wanted to make a new game, but didn't want to delete my save file on my original Sonic Advance 3 GBA cartridge I got 8 years ago. I really, really, REALLY just want to play that ONE game, and I want it to save. Sending the ROM from my DSTWO to the ez flash starts a new game every time, and sending the ROM from my DSTTi to the ez flash loads up a 100% completed save file, something I haven't been able to do for the past 8 years (that last Special Stage is hard..) so I don't know why one gives me no save while the other gives me a 100% completed save. Please, I really need help with this... Any help at all would be VERY appreciated.